OK here we go.
I have read the review and taken onboard what you have said. It's true that this is not an 'all bases covered' compact camera. It has it's strengths as well as it's weakneses. I believe it's strengths far outweigh any weakneses IMHO.
Some of it's weaknesses can be addressed by third party addons. I feel Canon really missed a trick with the ergonomics.
A third party grip made from machine grade aluminium can be purchased at...
http://www.kleptography.com/rf/#camera_s90
This simple stick on grip does wonders for ergonomics with the shutter finger naturualy falling into the correct position and thumb iinto the groove at the back. It also prevents you from hitting the rear wheel as often and allows you to get a sturdier grip on the camera. You can even hold it one handed with not too much fear of it slipping out of your hand. Highly recommended.
If you require the use of filters Lensmate now provide a stick on adapter allowing the use of 37mm filters.
http://www.lensmateonline.com/newsite/S90.html
Or on fleabay they do a S90 adapter tube that attaches to the hotshoe (Search for 'Canon S90 adapter').
Also get a spare battery. It is a no brainer.
As for cases it depends on preference. I just use an iPoo sock derivative and slide it in my pocket. Less bulk and protects it somewhat.
I never use the flash. I find it a waste of time and would only ever use it in emergencies. I turn it off by default and never use fully auto mode. If I need proper flash lighting I will use an optically triggered external flash handheld and set the internal flash to low.
BTW you forgot to mention that the included hand strap is complete crap. It's far too big and has no slider on it to make it more secure on your wrist. Dump it and use a third party wrist strap or use a neck strap like I do.
You also get exposure bracketing for HDR/Exposure blending. Very useful!
If you want to see what this baby can do and discuss further checkout thes following Flickr groups (Soon to be merged hopefully).
http://www.flickr.com/groups/canonpowershot_s90/
http://www.flickr.com/groups/canon_s90/